Re: [Bioc-devel] tximport fails to build on Windows

Hi Mike, Here is a more informative error from Stangling and sourcing the vignette on the Windows builder: ... reading in files with read_tsv 1 Error in file(con, "r") : cannot open the connection In addition: Warning message: In file(con, "r") : cannot open file

[Bioc-devel] segfault in csaw native code

Hi Aaron, I'm making a ChIP-Seq analyisis pipeline using csaw, and I'm running into an inconsistent error/segfault. I've reduced it to a test case which you can find here: https://www.dropbox.com/sh/2a2vpb5ek4413fx/AAAXwCaTzsAmfyPefwAbFg8Na?dl=0 The test case consists of my R workspace saved

Re: [Bioc-devel] The story of tracing a derfinder bug on OSX that sometimes popped up, sometimes it didn't. Related to IRanges/S4Vectors '$<-'

On 03/21/2017 08:21 PM, Hervé Pagès wrote: Hi Leonardo, Thanks for hunting down and isolating that bug! I tried to simplify your code even more and was able to get a segfault with just: setClass("A", representation(stuff="numeric")) x <- logical(10) x[TRUE] <- new("A") I get the

Re: [Bioc-devel] The story of tracing a derfinder bug on OSX that sometimes popped up, sometimes it didn't. Related to IRanges/S4Vectors '$<-'

Hi Leonardo, Thanks for hunting down and isolating that bug! I tried to simplify your code even more and was able to get a segfault with just: setClass("A", representation(stuff="numeric")) x <- logical(10) x[TRUE] <- new("A") I get the segfault about 50% of the time on a fresh R session

Re: [Bioc-devel] Citation of an accompanying paper

Hi Alina, I think you need to add a file named CITATION in your package (usually under the inst folder) and use bibentry as follows bibentry(bibtype = "Article", title = "Combining multiple tools outperforms individual methods in gene set enrichment analyses", author =

[Bioc-devel] The story of tracing a derfinder bug on OSX that sometimes popped up, sometimes it didn't. Related to IRanges/S4Vectors '$<-'

Hi bioc-devel, This is a story about a bug that took me a long time to trace. The behaviour was really weird, so I'm sharing the story in case this helps others in the future. I was originally writing it to request help, but then I was able to find the issue ^^. The story ends right now with code

Re: [Rd] Incompatible change in R-devel

On 21 March 2017 at 17:18, Prof Brian Ripley wrote: | On 21/03/2017 16:38, Dirk Eddelbuettel wrote: | > On 21 March 2017 at 07:29, Prof Brian Ripley wrote: | > | As of today's commit r72375 all packages with native-routine | > | registration of C or Fortran routines need to be reinstalled in

Re: [Rd] Error "Warning in read_symbols_from_dll(so, rarch): this requires 'objdump.exe' to be on the PATH

On 21/03/2017 17:12, Uwe Ligges wrote: On 19.03.2017 23:50, Christophe Genolini wrote: Hi all, I try to compile my package kml and I get the message [That will not be 'compiling': it may be from R CMD check, e.g. from wuth --as-cran in R-devel.] Warning in

Re: [Rd] Incompatible change in R-devel

On 21/03/2017 16:38, Dirk Eddelbuettel wrote: Hi Brian, On 21 March 2017 at 07:29, Prof Brian Ripley wrote: | As of today's commit r72375 all packages with native-routine | registration of C or Fortran routines need to be reinstalled in R-devel | (and that include some of the recommended

Re: [Rd] Error "Warning in read_symbols_from_dll(so, rarch): this requires 'objdump.exe' to be on the PATH

On 19.03.2017 23:50, Christophe Genolini wrote: Hi all, I try to compile my package kml and I get the message Warning in read_symbols_from_dll(so,rarch): this requires 'objdump.exe' to be on the PATH I check 'Writing R Extensions' but I did not find any reference to this error. Does someone

Re: [Rd] Hyperbolic tangent different results on Windows and Mac

On 21.03.2017 10:54, Martin Maechler wrote: Rodrigo Zepeda on Fri, 17 Mar 2017 12:56:06 -0600 writes: > Dear all, > We seem to have found a "strange" behaviour in the hyperbolic tangent > function tanh on Windows. > When running tanh(356 + 0i) the

Re: [Rd] Incompatible change in R-devel

Hi Brian, On 21 March 2017 at 07:29, Prof Brian Ripley wrote: | As of today's commit r72375 all packages with native-routine | registration of C or Fortran routines need to be reinstalled in R-devel | (and that include some of the recommended packages in R itself which | will not be

Re: [Bioc-devel] Package not being built on Windows or Mac

Thank you all for the explanations, and the assurance that Windows and Mac users should still be able to install it. Robert On Tue, Mar 21, 2017, 2:56 AM Hervé Pagès wrote: > On 03/20/2017 02:31 PM, Dan Tenenbaum wrote: > > As I recall, there were issues building

Re: [Rd] Hyperbolic tangent different results on Windows and Mac

> Rodrigo Zepeda > on Fri, 17 Mar 2017 12:56:06 -0600 writes: > Dear all, > We seem to have found a "strange" behaviour in the hyperbolic tangent > function tanh on Windows. > When running tanh(356 + 0i) the Windows result is NaN + 0.i while on

Re: [Rd] outer not applying a constant function

> William Dunlap > on Mon, 20 Mar 2017 10:20:11 -0700 writes: >> Or is this a bad idea? > I don't like the proposal. I have seen code like the following (in > fact, I have written such code, where I had forgotten a function was > not vectorized)

Re: [Bioc-devel] developing R package for new release

Thanks for taking the time to reply, James. I was confused by the fact that R 3.3.3 was released a few weeks ago and I was thinking that was previously the R-devel… meaning the R version you’re supposed to develop against would have just changed a few weeks ago. I re-read the sentence “R has

[Rd] Incompatible change in R-devel

As of today's commit r72375 all packages with native-routine registration of C or Fortran routines need to be reinstalled in R-devel (and that include some of the recommended packages in R itself which will not be reinstalled via make dependencies, so we advise a clean rebuild of R). We try

Re: [Bioc-devel] Package not being built on Windows or Mac

On 03/20/2017 02:31 PM, Dan Tenenbaum wrote: As I recall, there were issues building RCytoscape (and packages that depend on it) on Mac and Windows. Mostly because this requires a running instance of Cytoscape for each platform (and double that for release + devel). That used too much